Mitchell had run away from Rhyanna after she and her Misdreavus kept defeating him and his newly caught Murkrow. Rhyanna explained to Ash, Dawn, and Brock that it must have been his Murkrow that made illusions of Giratina and the flood that scared the group.
While looking for the Dusk Stone, Ash and Dawn encounter Mitchell's Murkrow again. When it attacked, Pikachu took it out with one Thunderbolt, enraging Mitchell. He explained that he was training Murkrow very hard without any rest so that it could become strong, but because of this, Murkrow stopped obeying him. Ash and Dawn explained to him that what he was doing wasn't right and Pokémon needed to be treated as partners. Mitchell began crying, realizing that he had hurt Murkrow.
Mitchell and Murkrow eventually returned to Rhyanna, only to find her in trouble. Team Rocket had stolen her Misdreavus and also attempted to take the Dusk Stone that she found. Mitchell helped his sister and Misdreavus escape from Team Rocket. Rhyanna no longer felt the need of evolving her Misdreavus into Mismagius, and she and her brother decided to battle for the Dusk Stone, awarding it to the victor of the best of ten battles.
Murkrow is Mitchell's only known Pokémon, and although it was powerful it was unable to defeat Rhyanna's Misdreavus in a battle. Running away to the mountains to train, Mitchell tried to teach Wing Attack to Murkrow by throwing stones at it. However, instead of learning the attack, Murkrow was hit by the stones and as a result stopped trusting Mitchell and ran away. During its time away, it would play pranks on travelers by causing hallucinations. Mitchell finally caught up with Murkrow when it was knocked out by Pikachu's Thunderbolt, and realized how much he had hurt Murkrow with his training methods. Later, Murkrow helped rescue Misdreavus from Team Rocket and Mitchell battled Rhyanna for the Dusk Stone she had found, knowing if he won he could evolve Murkrow into Honchkrow.